Syphacia muris

About Syphacia muris

The nematode Syphacia muris, or rat pinworm, is a parasite of rats.
The nematode Syphacia muris (Nematoda: Oxyuridae) is a ubiquitous nematode that commonly infects laboratory rodents (mainly rats). The direct transmission of this gastrointestinal nematode by contaminated food, water and bedding facilitates transmission in animal holdings. This results in continual re-exposure to the parasite, making the control of pinworms quite difficult and rodent colonies are frequently infected. Syphacia muris inhabits the caecum and the colon of the host.

Genome Assembly & Annotation

Assembly

The draft genome assembly was produced by the Parasite Genomic group at the Wellcome Trust Sanger Institute, in collaboration with Rafael Toledo (Universidad de Valencia) as part of the 50 Helminth Genomes project. The assembly uses Illumina paired-end sequencing followed by an in-house genome assembly pipeline comprising various steps, including contig assembly, scaffolding, gap-filling and error-correction.

Annotation

The gene predictions were made by the Parasite Genomics group at the Wellcome Trust Sanger Institute and WormBase, as part of the 50 Helminth Genomes project. An in-house pipeline was developed that used MAKER to generate high-quality annotations by integrating evidence from multiple sources: ab initio gene predictions from AUGUSTUS, GeneMark-ES, and SNAP; projected annotation from C. elegans (using GenBlastG) and the taxonomically nearest reference helminth genome (using RATT); and ESTs, mRNAs and proteins from related organisms aligned to the genome using BLAST, with refinement of alignments using Exonerate.